CombineEmbeddingsState

CombineEmbeddingsState

This step combines multiple embeddings from different modalities into a single matrix for downstream analysis. It wraps the scaleByNeighbors function from scran.js.

Methods not documented here are not part of the stable API and should not be used by applications.

Classes

CombineEmbeddingsState

Methods

compute(parameters)

Description:

  • This method should not be called directly by users, but is instead invoked by runAnalysis.

Source:
Parameters:
Name Type Description
parameters object

Parameter object, equivalent to the adt_normalization property of the parameters of runAnalysis.

Properties
Name Type Attributes Description
rna_weight number <optional>

Relative weight of the RNA embeddings.
adt_weight number <optional>

Relative weight of the ADT embeddings.
crispr_weight number <optional>

Relative weight of the CRISPR embeddings.
approximate boolean <optional>

Whether an approximate nearest neighbor search should be used by scaleByNeighbors.
Returns:

The object is updated with new results.

fetchCombined() → {Float64WasmArray}

Source:
Returns:

Buffer containing the combined embeddings as a column-major dense matrix, where the rows are the dimensions and the columns are the cells. This is available after running compute.

Type
Float64WasmArray

fetchNumberOfCells() → {number}

Source:
Returns:

Number of cells in fetchCombined, available after running compute.

Type
number

fetchNumberOfDimensions() → {number}

Source:
Returns:

Number of dimensions in fetchCombined, available after running compute.

Type
number

fetchParameters() → {object}

Source:
Returns:

Object containing the parameters.

Type
object

(static) defaults() → {object}

Source:
Returns:

Object containing default parameters, see the parameters argument in compute for details.

Type
object